Strain identifier

BacDive ID: 166282

Type strain: Yes

Species: Rhodoligotrophos defluvii

Strain Designation: lm1

NCBI tax ID(s): 2561934 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.1 (current version):
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 9.1 (current version)

General

@ref: 68241

BacDive-ID: 166282

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Rhodoligotrophos defluvii lm1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from PO saponification wastewater activated sludge.

NCBI tax id

  • NCBI tax id: 2561934
  • Matching level: species

doi: 10.13145/bacdive166282.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Parvibaculaceae
  • genus: Rhodoligotrophos
  • species: Rhodoligotrophos defluvii
  • full scientific name: Rhodoligotrophos defluvii Liu et al. 2019

@ref: 68241

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Hyphomicrobiales

family: Parvibaculaceae

genus: Rhodoligotrophos

species: Rhodoligotrophos defluvii

strain designation: lm1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
68241negative0.8-1.2 µm0.3-0.5 µmrod-shaped
69480negative96.571

colony morphology

  • @ref: 68241
  • colony size: 1.5 mm
  • colony color: red
  • colony shape: circular
  • incubation period: 4 days
  • medium used: LB (Luria-Bertani) agar

Culture and growth conditions

culture temp

@refgrowthtypetemperature
68241positivegrowth15-45
68241positiveoptimum40

culture pH

@refabilitytypepHPH range
68241positivegrowth4-10alkaliphile
68241positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 68241
  • oxygen tolerance: aerobe

spore formation

  • @ref: 68241
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
68241NaClpositivegrowth0-4 %(w/v)
68241NaClpositiveoptimum1-2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6824116947citrate+assimilation
6824129864mannitol+builds acid from
6824117113erythritol+builds acid from
6824117108D-arabinose+builds acid from
6824130849L-arabinose+builds acid from
6824116988D-ribose+builds acid from
6824165327D-xylose+builds acid from
6824165328L-xylose+builds acid from
6824115824D-fructose+builds acid from
682414853esculin+builds acid from
6824117266L-sorbose+builds acid from
6824118305arbutin+/-builds acid from
6824132528turanose+/-builds acid from
68241potassium 2-dehydro-D-gluconate+/-builds acid from
6824162318D-lyxose+builds acid from
6824116443D-tagatose+builds acid from
68241potassium 5-dehydro-D-gluconate+builds acid from
6824115963ribitol-builds acid from
6824174863methyl beta-D-xylopyranoside-builds acid from
6824112936D-galactose-builds acid from
6824117634D-glucose-builds acid from
6824116024D-mannose-builds acid from
6824162345L-rhamnose-builds acid from
6824116813galactitol-builds acid from
6824117268myo-inositol-builds acid from
6824129864mannitol-builds acid from
6824130911sorbitol-builds acid from
6824143943methyl alpha-D-mannoside-builds acid from
68241320061methyl alpha-D-glucopyranoside-builds acid from
68241506227N-acetyl-D-glucosamine-builds acid from
6824127613amygdalin-builds acid from
6824117814salicin-builds acid from
6824117057cellobiose-builds acid from
6824117306maltose-builds acid from
6824117716lactose-builds acid from
6824128053melibiose-builds acid from
6824117992sucrose-builds acid from
6824127082trehalose-builds acid from
6824115443inulin-builds acid from
682416731melezitose-builds acid from
6824116634raffinose-builds acid from
6824128017starch-builds acid from
6824117151xylitol-builds acid from
6824128087glycogen-builds acid from
6824128066gentiobiose-builds acid from
6824128847D-fucose-builds acid from
6824118287L-fucose-builds acid from
6824118333D-arabitol-builds acid from
6824118403L-arabitol-builds acid from
6824132032potassium gluconate-builds acid from
6824132528turanose+/-carbon source
6824117925alpha-D-glucose+/-carbon source
6824114314D-glucose 6-phosphate+/-carbon source
6824178697D-fructose 6-phosphate+/-carbon source
6824118183L-pyroglutamic acid+/-carbon source
6824132323glucuronamide+/-carbon source
68241168102-oxoglutarate+/-carbon source
6824115589L-malate+/-carbon source
6824116977L-alanine+carbon source
6824117115L-serine+carbon source
6824151850methyl pyruvate+carbon source
6824116865gamma-aminobutyric acid+carbon source
6824164552alpha-hydroxybutyrate+carbon source
68241167632-oxobutanoate+carbon source
682418295beta-hydroxybutyrate+carbon source
6824113705acetoacetate+/-carbon source
6824117272propionate+carbon source
6824116411acetic acid+carbon source
6824115740formate+carbon source
6824123652dextrin-carbon source
6824117306maltose-carbon source
6824127082trehalose-carbon source
6824117057cellobiose-carbon source
6824128066gentiobiose-carbon source
6824117992sucrose-carbon source
6824117164stachyose-carbon source
6824116634raffinose-carbon source
6824117716lactose-carbon source
6824128053melibiose-carbon source
6824137657methyl D-glucoside-carbon source
6824117814D-salicin-carbon source
68241506227N-acetyl-D-glucosamine-carbon source
6824163154N-acetyl-beta-D-mannosamine-carbon source
6824128037n-acetyl-D-galactosamine-carbon source
68241n-acetyl-neuraminic acid-carbon source
6824116024D-mannose-carbon source
6824115824D-fructose-carbon source
6824112936D-galactose-carbon source
68241739183-O-methyl-D-glucose-carbon source
6824128847D-fucose-carbon source
6824118287L-fucose-carbon source
6824162345L-rhamnose-carbon source
6824117596inosine-carbon source
6824117924D-sorbitol-carbon source
6824116899D-mannitol-carbon source
6824118333D-arabitol-carbon source
6824117268myo-inositol-carbon source
6824117754glycerol-carbon source
6824135391aspartate-carbon source
6824116523D-serine-carbon source
682415291gelatin-carbon source
6824170744glycyl-L-proline-carbon source
6824116467L-arginine-carbon source
6824129991L-aspartate-carbon source
6824129985L-glutamate-carbon source
6824115971L-histidine-carbon source
6824117309pectin-carbon source
6824118024D-galacturonic acid-carbon source
6824115895D-galactonic acid lactone-carbon source
682418391D-gluconate-carbon source
6824115748D-glucuronate-carbon source
6824135390galactarate-carbon source
6824117521(-)-quinic acid-carbon source
6824133801D-saccharate-carbon source
68241181014-hydroxyphenylacetic acid-carbon source
68241D-lactic acid methyl ester-carbon source
68241L-lactate-carbon source
6824116947citrate-carbon source
6824115588D-malate-carbon source
6824173706bromosuccinate-carbon source
6824153423tween 40-carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
682416104kanamycinyesyes
6824117698chloramphenicolyesyes
6824117076streptomycinyesyes
6824117833gentamicinyesyes
682417507neomycinyesyes
6824128971ampicillinyesyes
6824127902tetracyclineyesyes
682416472lincomycinyesyes
682413493cefoperazoneyesyes
682419215spectinomycinyesyes
682417935paromomycin sulfateyesyes
6824117334penicillinyesyes
6824148923erythromycinyesyes
6824126580rifamycinyesyes
682416472lincomycinyesyes
6824145735troleandomycinyesyes
6824150694minocyclineyesyes
6824128001vancomycinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
6824135581indoleno
6824116136hydrogen sulfideno
6824115688acetoinno

metabolite tests

  • @ref: 68241
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
68241catalase+1.11.1.6
68241cytochrome oxidase-1.9.3.1
68241beta-galactosidase-3.2.1.23
68241lysine decarboxylase-4.1.1.18
68241ornithine decarboxylase-4.1.1.17
68241tryptophan deaminase-4.1.99.1
68241arginine dihydrolase+3.5.3.6
68241urease+3.5.1.5
68241gelatinase+
68241leucine arylamidase+3.4.11.1
68241valine arylamidase+
68241cystine arylamidase+3.4.11.3
68241trypsin+3.4.21.4
68241chymotrypsin+3.4.4.5
68241acid phosphatase+3.1.3.2
68241naphthol-AS-BI-phosphohydrolase+
68241alkaline phosphatase+/-3.1.3.1
68241esterase (C 4)+/-
68241esterase Lipase (C 8)+/-
68241lipase (C 14)+/-
68241alpha-galactosidase-3.2.1.22
68241beta-glucuronidase-3.2.1.31
68241alpha-glucosidase-3.2.1.20
68241beta-glucosidase-3.2.1.21
68241N-acetyl-beta-glucosaminidase-3.2.1.52
68241alpha-mannosidase-3.2.1.24
68241beta-D-fucosidase-3.2.1.38

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68241C12:00.5
    68241C14:00.7
    68241C16:017
    68241C18:01.6
    68241C17:0 cyclo0.5
    68241C17:1 w8c0.1
    68241C18:1 w5c0.2
    68241C18:1 w7c29
    68241C19:0 cyclo w8c44.2
    68241C15:0 anteiso0.2
    68241C15:0 iso0.6
    68241C16:0 iso0.1
    68241C17:0 anteiso0.1
    68241C8:0 3OH0.2
    68241C16:0 2OH0.2
    68241C16:1 w7c/C16:1 w6c3.3
  • type of FA analysis: whole cell analysis
  • incubation medium: LB
  • incubation temperature: 37
  • software version: Sherlock 4.5
  • library/peak naming table: TSBA40
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

  • @ref: 68241
  • sample type: PO saponification wastewater activated sludge
  • geographic location: Binzhou, Shandong Province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 37.6564
  • longitude: 118.118
  • enrichment culture: LB
  • enrichment culture duration: 1 week
  • enrichment culture temperature: 37

Sequence information

16S sequences

  • @ref: 68241
  • description: Rhodoligotrophos defluvii strain lm1 16S ribosomal RNA gene, partial sequence
  • accession: MK124546
  • length: 1359
  • database: nuccore
  • NCBI tax ID: 1969729

Genome sequences

  • @ref: 68241
  • description: Rhodoligotrophos defluvii lm1
  • accession: GCA_005281615
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2561934

GC content

  • @ref: 68241
  • GC-content: 64.4
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno96.571yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.71yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes78.484no
69480spore-formingspore-formingAbility to form endo- or exosporesno81.25no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno91.21no
69480flagellatedmotile2+Ability to perform flagellated movementno52.191no

External links

@ref: 68241

culture collection no.: CCTCC AB 2019071, KCTC 72156

literature

  • topic: Phylogeny
  • Pubmed-ID: 31502947
  • title: Rhodoligotrophos defluvii sp. nov., isolated from activated sludge.
  • authors: Liu YL, Meng D, Li RR, Gu PF, Fan XY, Huang ZS, Du ZJ, Li Q
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003691
  • year: 2019
  • mesh: Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/analogs & derivatives/chemistry, Waste Water/microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
68241Yu-Ling Liu, Dong Meng, Rui-Rui Li, Peng-Fei Gu, Xiang-Yu Fan, Zhao-Song Huang, Zong-Jun Du and Qiang LiRhodoligotrophos defluvii sp. nov., isolated from activated sludge10.1099/ijsem.0.003691IJSEM 69: 3830-3836 2019
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes